NM_000051.4(ATM):c.186-7C>T AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Sep 18, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000589334.18

Allele description [Variation Report for NM_000051.4(ATM):c.186-7C>T]

NM_000051.4(ATM):c.186-7C>T

Gene:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.186-7C>T

HGVS:

NC_000011.10:g.108229171C>T
NG_009830.1:g.11340C>T
NM_000051.4:c.186-7C>TMANE SELECT
NM_001351834.2:c.186-7C>T
NM_001351835.2:c.186-7C>T
NM_001351836.2:c.186-7C>T
LRG_135t1:c.186-7C>T
LRG_135:g.11340C>T
NC_000011.9:g.108099898C>T
NM_000051.3:c.186-7C>T

Links:

dbSNP: rs55674039

NCBI 1000 Genomes Browser:

rs55674039

Molecular consequence:

NM_000051.4:c.186-7C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001351834.2:c.186-7C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001351835.2:c.186-7C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001351836.2:c.186-7C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000694202	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Mar 25, 2016)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 17517479, 12673804, 25980754, 25318351 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001473186	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Sep 18, 2023)	germline	clinical testing	Citation Link,
SCV001926578	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000694202

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Mar 25, 2016)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001473186

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Sep 18, 2023)

germline

clinical testing

Citation Link,

SCV001926578

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Possession of ATM sequence variants as predictor for late normal tissue responses in breast cancer patients treated with radiotherapy.

Ho AY, Fan G, Atencio DP, Green S, Formenti SC, Haffty BG, Iyengar P, Bernstein JL, Stock RG, Cesaretti JA, Rosenstein BS.

Int J Radiat Oncol Biol Phys. 2007 Nov 1;69(3):677-84. Epub 2007 May 22.

PubMed [citation]

PMID:: 17517479

ATM gene alterations in childhood acute lymphoblastic leukemias.

Gumy Pause F, Wacker P, Maillet P, Betts D, Sappino AP.

Hum Mutat. 2003 May;21(5):554. Erratum in: Hum Mutat. 2003 Sep;22(3):256.

PubMed [citation]

PMID:: 12673804

See all PubMed Citations (4)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694202.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

Variant summary: The c.186-7C>T variant affects a non-conserved intronic nucleotide. Mutation taster predicts benign outcome for this variant. 5/5 programs in Alamut predict no significant effect on RNA splicing sites. ESE finder predicts that this variant may affect ESE site of SRp40. However, these predictions are not validated by experimental studies yet. This variant is found in 149/83742 control chromosomes, predominantly observed in African subpopulation in ExAC with observed MAF of 0.01887 (139/7368 chr, 1 homozygote), This frequency exceeds the maximal expected frequency of a pathogenic allele (0.0005), suggesting this variant is a benign polymorphism especially for Africans. This variant has been reported in multiple pts with different kinds of cancers (including BrC, T-ALL, AML, LS associated cancer, etc.) without strong evidence for causality. In addition, two clinical laboratories via ClinVar classified this variant as benign, without evidence to independently evaluate. Taken together, this variant was classified as Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001473186.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001926578.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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